1S32

Molecular Recognition of the Nucleosomal 'Supergroove'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.219 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Molecular Recognition of the Nucleosomal 'Supergroove'

Edayathumangalam, R.S.Weyermann, P.Gottesfeld, J.M.Dervan, P.B.Luger, K.

(2004) Proc Natl Acad Sci U S A 101: 6864-6869

  • DOI: https://doi.org/10.1073/pnas.0401743101
  • Primary Citation of Related Structures:  
    1S32

  • PubMed Abstract: 

    Chromatin is the physiological substrate in all processes involving eukaryotic DNA. By organizing 147 base pairs of DNA into two tight superhelical coils, the nucleosome generates an architecture where DNA regions that are 80 base pairs apart on linear DNA are brought into close proximity, resulting in the formation of DNA "supergrooves." Here, we report the design of a hairpin polyamide dimer that targets one such supergroove. The 2-A crystal structure of the nucleosome-polyamide complex shows that the bivalent "clamp" effectively crosslinks the two gyres of the DNA superhelix, improves positioning of the DNA on the histone octamer, and stabilizes the nucleosome against dissociation. Our findings identify nucleosomal supergrooves as platforms for molecular recognition of condensed eukaryotic DNA. In vivo, supergrooves may foster synergistic protein-protein interactions by bringing two regulatory elements into juxtaposition. Because supergroove formation is independent of the translational position of the DNA on the histone octamer, accurate nucleosome positioning over regulatory elements is not required for supergroove participation in eukaryotic gene regulation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3C [auth A],
G [auth E]
135Xenopus laevisMutation(s): 0 
Gene Names: LOC121398065
UniProt
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Entity Groups  
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UniProt GroupP84233
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4D [auth B],
H [auth F]
102Xenopus laevisMutation(s): 0 
Gene Names: LOC121398084
UniProt
Find proteins for P62799 (Xenopus laevis)
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Go to UniProtKB:  P62799
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UniProt GroupP62799
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AE [auth C],
I [auth G]
119Xenopus laevisMutation(s): 0 
Gene Names: h2ac14.L
UniProt
Find proteins for P06897 (Xenopus laevis)
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UniProt GroupP06897
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2BF [auth D],
J [auth H]
122Xenopus laevisMutation(s): 0 
Gene Names: LOC108704303
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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Entity ID: 1
MoleculeChains LengthOrganismImage
palindromic alpha-satellite 146 bp DNA fragmentA [auth I],
B [auth J]
146Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OGG
Query on OGG

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TA [auth J]2-(2-CARBAMOYLMETHOXY-ETHOXY)-ACETAMIDE
C6 H12 N2 O4
XEXSGNBDGFXDDF-UHFFFAOYSA-N
IMT
Query on IMT

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CA [auth I],
EA [auth I],
R [auth I],
T [auth I]
4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID
C5 H7 N3 O2
PPQDQYBXCYQCNH-UHFFFAOYSA-N
PYB
Query on PYB

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DA [auth I]
FA [auth I]
HA [auth I]
IA [auth I]
JA [auth I]
DA [auth I],
FA [auth I],
HA [auth I],
IA [auth I],
JA [auth I],
KA [auth I],
S [auth I],
U [auth I],
W [auth I],
X [auth I],
Y [auth I],
Z [auth I]
4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID
C6 H8 N2 O2
MUEOQEUSJMFYHV-UHFFFAOYSA-N
ABU
Query on ABU

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GA [auth I],
V [auth I]
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
DIB
Query on DIB

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BA [auth I],
MA [auth I]
3-AMINO-(DIMETHYLPROPYLAMINE)
C5 H14 N2
IUNMPGNGSSIWFP-UHFFFAOYSA-N
BAL
Query on BAL

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AA [auth I],
LA [auth I]
BETA-ALANINE
C3 H7 N O2
UCMIRNVEIXFBKS-UHFFFAOYSA-N
MN
Query on MN

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K [auth I]
L [auth I]
M [auth I]
N [auth I]
NA [auth J]
K [auth I],
L [auth I],
M [auth I],
N [auth I],
NA [auth J],
O [auth I],
OA [auth J],
P [auth I],
PA [auth J],
Q [auth I],
QA [auth J],
RA [auth J],
SA [auth J],
WA [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

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UA [auth A],
VA [auth D],
XA [auth E],
YA [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.352α = 90
b = 109.717β = 90
c = 181.827γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-11
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection